BN0644 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 4 2.0660e-07 2.5679e-05
Layer 5 1.1509e-06 1.2427e-04
Layer 3 1.1572e-06 3.7825e-03
Layer 6 9.0887e-05 2.3416e-03
Layer 2 1.8544e-02 3.0369e-01
WM 4.1963e-01 4.1026e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
SNCA Expression Distribution
Gene Specificity Score (GSS)
SNCA GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
SNCA Layer 5 2.2168 0.7856
CLSTN3 Layer 5 2.5332 0.7425
NEUROD2 Layer 5 2.5059 0.7397
ACOT7 Layer 5 2.4727 0.7336
MAP2K4 Layer 5 2.4785 0.7332
TUBB3 Layer 4 2.4180 0.7316
RUSC1 Layer 4 2.5566 0.7300
NEGR1 Layer 4 2.6191 0.7299
REEP1 Layer 5 2.4395 0.7288
PFKP Layer 5 2.6426 0.7287
SLC6A17 Layer 4 2.3750 0.7282
SYNGR3 Layer 5 2.3555 0.7270
NUDT4 Layer 4 2.3125 0.7268
TBR1 Layer 4 2.5566 0.7262
NUAK1 Layer 4 2.4395 0.7249
GALNT17 Layer 4 2.4727 0.7247
PHF24 Layer 4 2.5605 0.7241
SCG3 Layer 4 2.4297 0.7241
TOM1L2 Layer 4 2.4668 0.7237
PPP2R2C Layer 4 2.4238 0.7232
TTC9B Layer 4 2.8145 0.7229
BRSK2 Layer 4 2.7363 0.7216
ATP13A2 Layer 5 2.3809 0.7207
RERE Layer 4 2.3965 0.7205
RAB11A Layer 5 2.1816 0.7202
ADD2 Layer 4 2.3965 0.7197
CPEB3 Layer 4 2.5391 0.7192
TSPAN13 Layer 4 2.3965 0.7187
NAP1L3 Layer 4 2.6016 0.7182
PCDH7 Layer 4 2.6191 0.7176
DYNLT3 Layer 5 2.4180 0.7174
BEX2 Layer 4 2.3125 0.7166
LIN7C Layer 4 2.5957 0.7161
UBE2QL1 Layer 5 2.5391 0.7159
KCNC2 Layer 5 2.5508 0.7153
MARF1 Layer 5 2.5059 0.7142
GABRG2 Layer 4 2.5781 0.7142
SLC25A22 Layer 5 2.5840 0.7139
HPCA Layer 4 2.8340 0.7135
PPP2R2B Layer 4 2.7246 0.7131
TCEAL2 Layer 4 2.4023 0.7123
STX1A Layer 5 2.6543 0.7122
SNAP91 Layer 4 2.5117 0.7119
APBA2 Layer 4 2.3652 0.7118
CAMK2G Layer 4 2.5117 0.7113
MTLN Layer 4 2.3027 0.7113
CDK14 Layer 4 2.5273 0.7112
NR1D1 Layer 4 2.8027 0.7110
LINGO1 Layer 5 2.3184 0.7100
RBFOX2 Layer 4 2.4668 0.7098

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN0644
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN0644_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0644/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0644/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0644/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0644/report/PD/BN0644_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0644/report/PD/BN0644_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 00:54:03
  • Number of Processes: 10
  • Spending Time: 0h 2m